Mutations in the Arabidopsis H3K4me2/3 demethylase jmj14 suppress posttranscriptional gene silencing by decreasing transgene transcription

Plant Cell

Volumn 24, Issue 9, 2012, Pages 3603-3612

  Le Masson, Ivan ^a   Jauvion, Vincent ^a   Bouteiller, Nathalie ^a   Rivard, Maud ^a   Elmayan, Taline ^a   Vaucheret, Hervé ^a  

^a INSTITUT JEAN PIERRE BOURGIN   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84868089374     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.112.103119     Document Type: Article

References (54)

1. Angel, A., Song, J., Dean, C., and Howard, M. (2011). A Polycombbased switch underlying quantitative epigenetic memory. Nature 476: 105-108.
2. Bannister, A.J., and Kouzarides, T. (2011). Regulation of chromatin by histone modifications. Cell Res. 21: 381-395.
3. Baumberger, N., and Baulcombe, D.C. (2005). Arabidopsis ARGONAUTE1 is an RNA slicer that selectively recruits microRNAs and short interfering RNAs. Proc. Natl. Acad. Sci. USA 102: 11928- 11933.
4. Berr, A., Shafiq, S., and Shen, W.-H. (2011). Histone modifications in transcriptional activation during plant development. Biochim. Biophys. Acta 1809: 567-576.
5. Berretta, J., Pinskaya, M., and Morillon, A. (2008). A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev. 22: 615-626.
6. Blevins, T., Rajeswaran, R., Shivaprasad, P.V., Beknazariants, D., Si-Ammour, A., Park, H.S., Vazquez, F., Robertson, D., Meins, F., JrHohn, T., and Pooggin, M.M. (2006). Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res. 34: 6233-6246.
7. Bouché, N., Lauressergues, D., Gasciolli, V., and Vaucheret, H. (2006). An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J. 25: 3347-3356.
8. Boutet, S., Vazquez, F., Liu, J., Béclin, C., Fagard, M., Gratias, A., Morel, J.B., Crété, P., Chen, X., and Vaucheret, H. (2003). Arabidopsis HEN1: A genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr. Biol. 13: 843-848.
9. Brosnan, C.A., Mitter, N., Christie, M., Smith, N.A., Waterhouse, P.M., and Carroll, B.J. (2007). Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc. Natl. Acad. Sci. USA 104: 14741-14746.
10. Dalmay, T., Hamilton, A., Rudd, S., Angell, S., and Baulcombe, D.C. (2000). An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101: 543-553.
11. Dalmay, T., Horsefield, R., Braunstein, T.H., and Baulcombe, D.C. (2001). SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis. EMBO J. 20: 2069-2078.
12. Deleris, A., Gallego-Bartolome, J., Bao, J., Kasschau, K.D., Carrington, J.C., and Voinnet, O. (2006). Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313: 68-71.
13. Deleris, A., Greenberg, M.V., Ausin, I., Law, R.W., Moissiard, G., Schubert, D., and Jacobsen, S.E. (2010). Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation. EMBO Rep. 11: 950-955.
14. Ding, S.-W., and Voinnet, O. (2007). Antiviral immunity directed by small RNAs. Cell 130: 413-426.
15. Dunoyer, P., Himber, C., Ruiz-Ferrer, V., Alioua, A., and Voinnet, O. (2007). Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways. Nat. Genet. 39: 848-856.
16. Dunoyer, P., Himber, C., and Voinnet, O. (2005). DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat. Genet. 37: 1356-1360.
17. Dunoyer, P., Schott, G., Himber, C., Meyer, D., Takeda, A., Carrington, J.C., and Voinnet, O. (2010). Small RNA duplexes function as mobile silencing signals between plant cells. Science 328: 912-916.
18. Elmayan, T., Adenot, X., Gissot, L., Lauressergues, D., Gy, I., and Vaucheret, H. (2009). A neomorphic sgs3 allele stabilizing miRNA cleavage products reveals that SGS3 acts as a homodimer. FEBS J. 276: 835-844.
19. Elmayan, T., Balzergue, S., Béon, F., Bourdon, V., Daubremet, J., Guénet, Y., Mourrain, P., Palauqui, J.C., Vernhettes, S., Vialle, T., Wostrikoff, K., and Vaucheret, H. (1998). Arabidopsis mutants impaired in cosuppression. Plant Cell 10: 1747-1758.
20. Fagard, M., Boutet, S., Morel, J.B., Bellini, C., and Vaucheret, H. (2000). AGO1, QDE-2, and RDE-1 are related proteins required for posttranscriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc. Natl. Acad. Sci. USA 97: 11650-11654.
21. Fusaro, A.F., Matthew, L., Smith, N.A., Curtin, S.J., Dedic-Hagan, J., Ellacott, G.A., Watson, J.M., Wang, M.-B., Brosnan, C., Carroll, B.J., and Waterhouse, P.M. (2006). RNA interferenceinducing hairpin RNAs in plants act through the viral defence pathway. EMBO Rep. 7: 1168-1175.
22. García-Alai, M.M., Allen, M.D., Joerger, A.C., and Bycroft, M. (2010). The structure of the FYR domain of transforming growth factor beta regulator 1. Protein Sci. 19: 1432-1438.
23. Gazzani, S., Lawrenson, T., Woodward, C., Headon, D., and Sablowski, R. (2004). A link between mRNA turnover and RNA interference in Arabidopsis. Science 306: 1046-1048.
24. Gendrel, A.V., Lippman, Z., Martienssen, R., and Colot, V. (2005). Profiling histone modification patterns in plants using genomic tiling microarrays. Nat. Methods 2: 213-218.
25. Gendrel, A.V., Lippman, Z., Yordan, C., Colot, V., and Martienssen, R.A. (2002). Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297: 1871- 1873.
26. Gy, I., Gasciolli, V., Lauressergues, D., Morel, J.B., Gombert, J., Proux, F., Proux, C., Vaucheret, H., and Mallory, A.C. (2007). Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors. Plant Cell 19: 3451-3461.
27. Hernandez-Pinzon, I., Yelina, N.E., Schwach, F., Studholme, D.J., Baulcombe, D., and Dalmay, T. (2007). SDE5, the putative homologue of a human mRNA export factor, is required for transgene silencing and accumulation of trans-acting endogenous siRNA. Plant J. 50: 140-148.
28. Jauvion, V., Elmayan, T., and Vaucheret, H. (2010). The conserved RNA trafficking proteins HPR1 and TEX1 are involved in the production of endogenous and exogenous small interfering RNA in Arabidopsis. Plant Cell 22: 2697-2709.
29. Jeong, J.-H., Song, H.-R., Ko, J.-H., Jeong, Y.-M., Kwon, Y.E., Seol, J.H., Amasino, R.M., Noh, B., and Noh, Y.-S. (2009). Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis. PLoS ONE 4: e8033.
30. Kim, T., and Buratowski, S. (2009). Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 59 transcribed regions. Cell 137: 259-272.
31. Kloc, A., and Martienssen, R. (2008). RNAi, heterochromatin and the cell cycle. Trends Genet. 24: 511-517.
32. Kuo, M.H., Brownell, J.E., Sobel, R.E., Ranalli, T.A., Cook, R.G., Edmondson, D.G., Roth, S.Y., and Allis, C.D. (1996). Transcription- linked acetylation by Gcn5p of histones H3 and H4 at specific lysines. Nature 383: 269-272.
33. Li, J., Yang, Z., Yu, B., Liu, J., and Chen, X. (2005). Methylation protects miRNAs and siRNAs from a 39-end uridylation activity in Arabidopsis. Curr. Biol. 15: 1501-1507.
34. Liu, X., Yu, C.W., Duan, J., Luo, M., Wang, K., Tian, G., Cui, Y., and Wu, K. (2012). HDA6 directly interacts with DNA methyltransferase MET1 and maintains transposable element silencing in Arabidopsis. Plant Physiol. 158: 119-129.
35. Lu, F., Cui, X., Zhang, S., Liu, C., and Cao, X. (2010). JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res. 20: 387-390.
36. Lu, F., Li, G., Cui, X., Liu, C., Wang, X.-J., and Cao, X. (2008). Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J. Integr. Plant Biol. 50: 886-896.
37. Mallory, A.C., and Vaucheret, H. (2006). Functions of microRNAs and related small RNAs in plants. Nat. Genet. 38 (Suppl): S31-S36.
38. Mallory, A.C., and Vaucheret, H.E. (2009). ARGONAUTE 1 homeostasis invokes the coordinate action of the microRNA and siRNA pathways. EMBO Rep. 10: 521-526.
39. Moehs, C.P., McElwain, E.F., and Spiker, S. (1988). Chromosomal proteins of Arabidopsis thaliana. Plant Mol. Biol. 11: 507-515.
40. Morel, J.B., Godon, C., Mourrain, P., Béclin, C., Boutet, S., Feuerbach, F., Proux, F., and Vaucheret, H. (2002). Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell 14: 629-639.
41. Morel, J.B., Mourrain, P., Béclin, C., and Vaucheret, H. (2000). DNA methylation and chromatin structure affect transcriptional and posttranscriptional transgene silencing in Arabidopsis. Curr. Biol. 10: 1591-1594.
42. Mourrain, P., et al. (2000). Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533-542.
43. Palauqui, J.C., Elmayan, T., Pollien, J.M., and Vaucheret, H. (1997). Systemic acquired silencing: Transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to nonsilenced scions. EMBO J. 16: 4738-4745.
44. Pinskaya, M., and Morillon, A. (2009). Histone H3 lysine 4 di-methylation: A novel mark for transcriptional fidelity? Epigenetics 4: 302-306.
45. Searle, I.R., Pontes, O., Melnyk, C.W., Smith, L.M., and Baulcombe, D.C. (2010). JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev. 24: 986-991.
46. Smith, L.M., Pontes, O., Searle, I., Yelina, N., Yousafzai, F.K., Herr, A.J., Pikaard, C.S., and Baulcombe, D.C. (2007). An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 19: 1507-1521.
47. Smith, N.A., Singh, S.P., Wang, M.B., Stoutjesdijk, P.A., Green, A.G., and Waterhouse, P.M. (2000). Total silencing by intronspliced hairpin RNAs. Nature 407: 319-320.
48. Souret, F.F., Kastenmayer, J.P., and Green, P.J. (2004). AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol. Cell 15: 173-183.
49. Taverna, S.D., Li, H., Ruthenburg, A.J., Allis, C.D., and Patel, D.J. (2007). How chromatin-binding modules interpret histone modifications: Lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14: 1025-1040.
50. Voinnet, O. (2009). Origin, biogenesis, and activity of plant micro- RNAs. Cell 136: 669-687.
51. Voinnet, O., Vain, P., Angell, S., and Baulcombe, D.C. (1998). Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell 95: 177-187.
52. Yang, W., Jiang, D., Jiang, J., and He, Y. (2010). A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis. Plant J. 62: 663-673.
53. Yoshikawa, M., Peragine, A., Park, M.Y., and Poethig, R.S. (2005). A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 19: 2164-2175.
54. Yu, B., Yang, Z., Li, J., Minakhina, S., Yang, M., Padgett, R.W., Steward, R., and Chen, X. (2005). Methylation as a crucial step in plant microRNA biogenesis. Science 307: 932-935.